1R1X | pdb_00001r1x

Crystal structure of oxy-human hemoglobin Bassett at 2.15 angstrom

PDB DOI: https://doi.org/10.2210/pdb1R1X/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Homo sapiens
Mutation(s): Yes

Deposited: 2003-09-25 Released: 2003-10-07
Deposition Author(s): Abdulmalik, O., Safo, M.K., Lerner, N.B., Ochotorena, J., Dhaikin, Y., Abraham, D.J., Asakura, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.288 (Depositor), 0.277 (DCC)
R-Value Work:
0.222 (Depositor), 0.215 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Characterization of hemoglobin bassett (alpha94Asp-->Ala), a variant with very low oxygen affinity

Abdulmalik, O., Safo, M.K., Lerner, N.B., Ochotorena, J., Daikhin, Y., Lakka, V., Santacroce, R., Abraham, D.J., Asakura, T.

(2004) Am J Hematol 77: 268-276

PubMed: 15495251 Search on PubMed
DOI: https://doi.org/10.1002/ajh.20184
Primary Citation Related Structures:
1R1X, 1R1Y

PubMed Abstract:
Hemoglobin (Hb) Bassett, an abnormal Hb variant with a markedly reduced oxygen affinity, was discovered in a Caucasian (Anglo-Saxon) male child who experienced episodes of cyanosis. Cation-exchange and reversed-phase (RP) high-performance liquid chromatography (HPLC) showed that the patient has an abnormal Hb, with a mutation in the alpha-globin. Tryptic peptide digest of the abnormal alpha-globin with subsequent HPLC analysis revealed abnormal elution of the alpha-T11 peptide. Further studies with Edman sequencing and electrospray mass spectrometry of tryptic peptide alpha-T11, as well as structural analysis by X-ray crystallography revealed an Asp-->Ala substitution at the alpha94 (G1) position, a match for Hb Bassett. Detailed functional studies showed that this Hb variant had a markedly reduced oxygen affinity (P(50) at pH 7.0 = 22 mmHg; Hb A P(50) = 10.5 mmHg), reduced Bohr effect (-0.26 compared to - 0.54 in Hb A), and low subunit cooperativity (n = 1.4, compared to 2.6 in Hb A). X-ray crystallography results explain the probable effects of the structural modification on the oxygen-binding properties of this Hb variant.

Organizational Affiliation

Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.

Macromolecule Content

Total Structure Weight: 32.47 kDa
Atom Count: 2,485
Modeled Residue Count: 287
Deposited Residue Count: 287
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin alpha chain	A	141	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905 Go to UniProtKB: P69905
PHAROS: P69905 GTEx: ENSG00000188536 ENSG00000206172
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69905
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin beta chain	B	146	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871 Go to UniProtKB: P68871
PHAROS: P68871 GTEx: ENSG00000244734
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68871
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
MBN Query on MBN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	TOLUENE C₇ H₈ YXFVVABEGXRONW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
CMO Query on CMO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.288 (Depositor), 0.277 (DCC)
R-Value Work: 0.222 (Depositor), 0.215 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.357	α = 90
b = 53.357	β = 90
c = 191.781	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
bioteX	data reduction
bioteX	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-10-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-10-07
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2018-08-29
Changes: Data collection, Database references
Version 1.5: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description